The New Clayden pp. 328 – 381

p. 330 — Nice. An explanation of exactly how you determine Sn1 and Sn2 kinetically — often not explicitly given.  Good to see it here.

 The illustrations in the book that I comment on can be reached on the web by substituting the page number I give for xx in the following

p. 335 — “one C-H bond of each methyl group must be parallel to one lobe of the empty p orbital at any one time”  Not so.  The methyl group could be disposed so that two of its hydrogen sigma bonds were 30 degrees away from the central carbon p orbital with one of them 90 degrees away.

p. 341 — “In the transition state, the carbon atom in the middle has a p orbital that shares one pair of electrons between the old and new bonds.”  So there is a change in hybridization of the central carbon in the transition state.  Also this is a 3 atom two electron ‘bond’ like those in B2H6.  Interesting. 

p. 343 — ‘Just like an umbrella in a high wind’  — great analogy (I used it myself many times, and it was fun to see their light bulbs switch on as students first understood exactly what is going on in Sn2).

p. 343 — I don’t understand how SOClF in SbF5 forms the secondary butyl cation from 2 butanol.  Is this an error, or am I dense?  Maybe if they start with 2 Fluoro butane it might work.

p. 346 — The difference in rates for Sn1 and Sn2 is all very nice, but the book doesn’t give any clue as to how much of a change in the free energy of activation these differences represent.  I’m going to try and find a calculation (in Anslyn).  As I recall, just as small changes in deltaG change the equilibrium constant markedly, small changes in the free energy of activation change rates by orders of magnitude. 

This is why computational chemistry is so hard, they calculate the energy of structures (which is usually large), when what we’re interested in here, is difference between two large quantities.   

p. 348 — Why not give actual values for bond strengths?  The P=O bond is very strong at 137 kiloCalories/mole (573 kiloJoules/mole), much stronger than a C-C bond (90 tops).

p. 350 — The animation of the Mitsunobu reaction is not to be missed.  It’s complicated with lots of atoms moving about, although PMe3 rather than PAr3 is used.  You can rotate the complex of PMe3 and DEAD to watch the reaction from any angle.  The animation of stage III is particularly impressive — lots of atoms dancing around, along with the ability to watch the action from any angle you wish.  

p. 354 — How does triphyenyl phosphine + water change N3 into NH2?

p. 354 — So why are thiols more acidic than water?  Probably because it is easier to stabilize a large anion than a small one (the negative charge is less concentrated, making the anion easier to solvate).

p. 356 — However, that’s not why SH is a better nucleophile (although it might be — they never discuss polarizability) it has to do with the energy match between HOMO and LUMO.  However although thay say soft nucleophiles are neutral only one of the 3 examples they give actually is (R3P:), while the other two (I-, RS-) are charged.

p. 361 — The animations here don’t show the bonds rotating (at least on my computer).

p. 367 — “Notice how in the smaller rings the bonds curve outwards, while in the larger rings the bonds curve inwards.”  What is the evidence for this? 

p. 373 — I’ve never really had a good mental handle on the ‘twist-boat’ structure.  However, even the animation doesn’t seem to capture it, or the half chair either.  This is even when stepping through the animation frame by frame. 

p. 374 — “For example, on a 400 MHz spectrometer, two signals separated by .5 ppm will be 100 Hertz apart”.  This is false.  Either 100 should be 200 or .5 should be .25.

p. 378 — The animation of the ring inversion of cis decalin doesn’t have enough frames to see what is going on (how quickly we become spoiled). 

p. 379 — All the bile acids are cis between rings A and B.  Why? — this is so they don’t pack together so well, and can dissolve lipids.  Their carboxylic acids makes them amphipathic (containing hydrophobic lipid and hydrophilic domains). 
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